Old quicktime with flash layer + adobe media encoder

Hi,
I have some quicktime .mov files.
These play fine in the older quicktime 6
They do not play in the newer quicktime 7
I posted about this issue at a Quicktime forum and discovered it is an issue with the flash layer in the newer quicktime.
These files do not display in Adobe Media Encoder.
My question is how is Adobe Media encoder affected by the Quicktime codecs?
Would removing Quicktime 7 from my machine and installing an older version effect AME?
Would it then be able to se the files and encode them to f4v?
If not are there any other solutions?
Rather desperate, I am doing a site for an animator and all the content I have been provided with is like this.
I could send a sample file if needed
Thanks
mark

Anders,
I have to make sure we are talking about the same thing. In the Effects Control Panel, you twirled open the Opacity intrinsic effect and clicked on the stopwatch to create a keyframe, correct?
I ask this because you can also adjust the Opacity by using the clip's opacity "rubber band" in the timeline, but no keyframes get added there unless you use the Pen tool or a modifier key in combination with the selection tool.
For the workaround to fix the issue, a keyframe has to be created.
-Jeff
PS - You're welcome. :)

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